Molecular phylogenies can be constructed from optimal
(algorithm-defined) alignments of amino acid sequences or of nucleotide
sequences. Some folks construct phylogenies based on each. The two
phylogenetic trees may differ from one another. Novices will often
interpret these differences with regard to coding vs. non-coding
changes, while experts will recognize that the alignments on which the
trees are based are not necessarily equivalent.
Is there software that can:
1) Given an amino acid sequence alignment and the raw nucleotide
sequences that translate to the amino acid sequences, produce a
nucleotide sequence alignment that is equivalent to the amino acid
sequence alignment; and/or
2) Given a nucleotide sequence alignment, translate the constituent
sequences into aligned amino acid sequences, so that the resulting amino
acid sequence alignment is equivalent to the nucleotide sequence
alignment?
If such software does not exist, should it?
Ulrich Melcher umelcher at bmb-fs1.biochem.okstate.edu
Department of Biochemistry
and Molecular Biology Tel: 405-744-6210
246 NRC FAX: 405-744-7799
Oklahoma State University
Stillwater OK 74078-3035 USA